derive_GeoMx_background {SpatialDecon} | R Documentation

## Derive background at the scale of the normalized data for GeoMx data

### Description

Estimates per-datapoint background levels from a GeoMx experiment. In studies with two or more probe pools, different probes will have different background levels. This function provides a convenient way to account for this phenomenon.

### Usage

    derive_GeoMx_background(norm, probepool, negnames)

### Arguments

`norm` | Matrix of normalized data, genes in rows and segments in columns. Must include negprobes, and must have rownames.
`probepool` | Vector of probe pool names for each gene, aligned to the rows of "norm".
`negnames` | Names of all negProbes in the dataset. Must be at least one neg.name within each probe pool.

### Value

A matrix of expected background values, in the same scale and dimensions as the "norm" argument.

### Examples

    data(mini_geomx_dataset)
    # estimate background:
    mini_geomx_dataset$bg <- derive_GeoMx_background(
      norm = mini_geomx_dataset$normalized,
      probepool = rep(1, nrow(mini_geomx_dataset$normalized)),
      negnames = "NegProbe"
    )

[Package SpatialDecon version 1.4.3 Index]